Starting phenix.real_space_refine
on Tue Feb 11 16:35:43 2025 by dcliebschner
===============================================================================

Processing files:
-------------------------------------------------------------------------------

  Found model, /net/cci-nas-00/data/ceres_data/9bfr_44504/02_2025/9bfr_44504.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9bfr_44504/02_2025/9bfr_44504.map

Processing PHIL parameters:
-------------------------------------------------------------------------------

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.19
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9bfr_44504/02_2025/9bfr_44504.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9bfr_44504/02_2025/9bfr_44504.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9bfr_44504/02_2025/9bfr_44504.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9bfr_44504/02_2025/9bfr_44504.cif"
  }
  resolution = 3.19
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


Starting job
===============================================================================
-------------------------------------------------------------------------------
Citation:
*********
Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams
PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography.
Acta Cryst. D74:531-544.

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.033
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      42      5.16       5
     C    4006      2.51       5
     N    1026      2.21       5
     O    1192      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 18 residue(s): 0.05s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib"
  Total number of atoms: 6266
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "A"
      Number of atoms: 3091
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 383, 3091
          Classifications: {'peptide': 383}
          Incomplete info: {'truncation_to_alanine': 3}
          Link IDs: {'PTRANS': 10, 'TRANS': 372}
          Chain breaks: 4
          Unresolved non-hydrogen bonds: 17
          Unresolved non-hydrogen angles: 21
          Unresolved non-hydrogen dihedrals: 17
          Planarities with less than four sites: {'PHE:plan': 1, 'HIS:plan': 1}
          Unresolved non-hydrogen planarities: 11
    Chain: "B"
      Number of atoms: 3091
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 383, 3091
          Classifications: {'peptide': 383}
          Incomplete info: {'truncation_to_alanine': 3}
          Link IDs: {'PTRANS': 10, 'TRANS': 372}
          Chain breaks: 4
          Unresolved non-hydrogen bonds: 17
          Unresolved non-hydrogen angles: 21
          Unresolved non-hydrogen dihedrals: 17
          Planarities with less than four sites: {'PHE:plan': 1, 'HIS:plan': 1}
          Unresolved non-hydrogen planarities: 11
    Chain: "A"
      Number of atoms: 42
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 42
          Unusual residues: {'NAG': 3}
          Classifications: {'undetermined': 3}
          Link IDs: {None: 2}
          Unresolved non-hydrogen bonds: 3
          Unresolved non-hydrogen angles: 6
          Unresolved non-hydrogen dihedrals: 9
          Unresolved non-hydrogen chiralities: 3
    Chain: "B"
      Number of atoms: 42
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 42
          Unusual residues: {'NAG': 3}
          Classifications: {'undetermined': 3}
          Link IDs: {None: 2}
          Unresolved non-hydrogen bonds: 3
          Unresolved non-hydrogen angles: 6
          Unresolved non-hydrogen dihedrals: 9
          Unresolved non-hydrogen chiralities: 3
  Time building chain proxies: 4.70, per 1000 atoms: 0.75
  Number of scatterers: 6266
  At special positions: 0
  Unit cell: (97.11, 98.77, 89.64, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      42     16.00
     O    1192      8.00
     N    1026      7.00
     C    4006      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=6, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 112 " - pdb=" SG  CYS A 201 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 282 " - pdb=" SG  CYS A 501 " distance=2.04
    Simple disulfide: pdb=" SG  CYS A 389 " - pdb=" SG  CYS A 403 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 112 " - pdb=" SG  CYS B 201 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 282 " - pdb=" SG  CYS B 501 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 389 " - pdb=" SG  CYS B 403 " distance=2.03

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Links applied
    NAG-ASN
      " NAG A 601 " - " ASN A 183 "
      " NAG A 602 " - " ASN A 474 "
      " NAG A 603 " - " ASN A 485 "
      " NAG B 601 " - " ASN B 183 "
      " NAG B 602 " - " ASN B 474 "
      " NAG B 603 " - " ASN B 485 "
  Time building additional restraints: 1.35
  Conformation dependent library (CDL) restraints added in 862.8 milliseconds
  

  1492 Ramachandran restraints generated.
    746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1480

  Finding SS restraints...
    Secondary structure from input PDB file:
      29 helices and 9 sheets defined
      37.1% alpha, 16.1% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.75
  Creating SS restraints...
    Processing helix  chain 'A' and resid 109 through 115
      removed outlier: 3.685A  pdb=" N   LEU A 113 " --> pdb=" O   PRO A 109 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 131 through 135
      removed outlier: 3.667A  pdb=" N   GLU A 134 " --> pdb=" O   LYS A 131 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 152 through 166
      removed outlier: 3.525A  pdb=" N   LEU A 156 " --> pdb=" O   PRO A 152 " (cutoff:3.500A)
      removed outlier: 3.556A  pdb=" N   PHE A 157 " --> pdb=" O   ASP A 153 " (cutoff:3.500A)
      removed outlier: 3.737A  pdb=" N   VAL A 158 " --> pdb=" O   SER A 154 " (cutoff:3.500A)
      removed outlier: 3.569A  pdb=" N   ILE A 159 " --> pdb=" O   ALA A 155 " (cutoff:3.500A)
      removed outlier: 3.652A  pdb=" N   ASN A 163 " --> pdb=" O   ILE A 159 " (cutoff:3.500A)
      removed outlier: 3.598A  pdb=" N   ALA A 165 " --> pdb=" O   ARG A 161 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 186 through 199
      removed outlier: 3.683A  pdb=" N   ILE A 192 " --> pdb=" O   GLU A 188 " (cutoff:3.500A)
      removed outlier: 3.532A  pdb=" N   VAL A 195 " --> pdb=" O   LEU A 191 " (cutoff:3.500A)
      removed outlier: 3.531A  pdb=" N   GLN A 199 " --> pdb=" O   VAL A 195 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 211 through 218
      removed outlier: 3.644A  pdb=" N   GLN A 217 " --> pdb=" O   GLU A 213 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 218 through 226
      removed outlier: 3.996A  pdb=" N   LYS A 223 " --> pdb=" O   GLU A 219 " (cutoff:3.500A)
      removed outlier: 3.889A  pdb=" N   ASP A 224 " --> pdb=" O   SER A 220 " (cutoff:3.500A)
      removed outlier: 3.590A  pdb=" N   GLU A 226 " --> pdb=" O   ILE A 222 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 235 through 249
      Proline residue:  A 241  - end of helix
      removed outlier: 3.505A  pdb=" N   LEU A 246 " --> pdb=" O   LYS A 242 " (cutoff:3.500A)
      removed outlier: 3.816A  pdb=" N   GLN A 249 " --> pdb=" O   HIS A 245 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 266 through 279
      removed outlier: 3.602A  pdb=" N   GLU A 279 " --> pdb=" O   ALA A 275 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 363 through 369
    Processing helix  chain 'A' and resid 370 through 385
      removed outlier: 3.653A  pdb=" N   ILE A 375 " --> pdb=" O   ALA A 371 " (cutoff:3.500A)
      removed outlier: 3.792A  pdb=" N   ASP A 376 " --> pdb=" O   GLY A 372 " (cutoff:3.500A)
      removed outlier: 3.826A  pdb=" N   TRP A 380 " --> pdb=" O   ASP A 376 " (cutoff:3.500A)
      removed outlier: 3.814A  pdb=" N   GLY A 383 " --> pdb=" O   ASN A 379 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 399 through 403
    Processing helix  chain 'A' and resid 409 through 414
      removed outlier: 4.036A  pdb=" N   TRP A 413 " --> pdb=" O   ILE A 410 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 423 through 431
    Processing helix  chain 'A' and resid 433 through 438
      removed outlier: 3.777A  pdb=" N   GLY A 437 " --> pdb=" O   ARG A 434 " (cutoff:3.500A)
      removed outlier: 4.081A  pdb=" N   THR A 438 " --> pdb=" O   LYS A 435 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 495 through 499
    Processing helix  chain 'B' and resid 109 through 115
      removed outlier: 3.703A  pdb=" N   LEU B 113 " --> pdb=" O   PRO B 109 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 131 through 135
      removed outlier: 4.314A  pdb=" N   PHE B 135 " --> pdb=" O   LYS B 131 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 131 through 135'
    Processing helix  chain 'B' and resid 151 through 166
      removed outlier: 3.908A  pdb=" N   ALA B 155 " --> pdb=" O   ASP B 151 " (cutoff:3.500A)
      removed outlier: 3.608A  pdb=" N   VAL B 158 " --> pdb=" O   SER B 154 " (cutoff:3.500A)
      removed outlier: 3.603A  pdb=" N   ILE B 159 " --> pdb=" O   ALA B 155 " (cutoff:3.500A)
      removed outlier: 3.719A  pdb=" N   ASN B 163 " --> pdb=" O   ILE B 159 " (cutoff:3.500A)
      removed outlier: 3.569A  pdb=" N   ALA B 165 " --> pdb=" O   ARG B 161 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 186 through 199
      removed outlier: 3.694A  pdb=" N   ILE B 192 " --> pdb=" O   GLU B 188 " (cutoff:3.500A)
      removed outlier: 3.508A  pdb=" N   VAL B 195 " --> pdb=" O   LEU B 191 " (cutoff:3.500A)
      removed outlier: 3.589A  pdb=" N   GLN B 199 " --> pdb=" O   VAL B 195 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 211 through 218
      removed outlier: 3.634A  pdb=" N   GLN B 217 " --> pdb=" O   GLU B 213 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 218 through 226
      removed outlier: 4.019A  pdb=" N   LYS B 223 " --> pdb=" O   GLU B 219 " (cutoff:3.500A)
      removed outlier: 3.814A  pdb=" N   ASP B 224 " --> pdb=" O   SER B 220 " (cutoff:3.500A)
      removed outlier: 3.592A  pdb=" N   GLU B 226 " --> pdb=" O   ILE B 222 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 235 through 249
      Proline residue:  B 241  - end of helix
      removed outlier: 3.506A  pdb=" N   LEU B 246 " --> pdb=" O   LYS B 242 " (cutoff:3.500A)
      removed outlier: 3.801A  pdb=" N   GLN B 249 " --> pdb=" O   HIS B 245 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 266 through 279
      removed outlier: 3.595A  pdb=" N   GLU B 279 " --> pdb=" O   ALA B 275 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 363 through 385
      removed outlier: 3.694A  pdb=" N   PHE B 370 " --> pdb=" O   ARG B 366 " (cutoff:3.500A)
      removed outlier: 4.020A  pdb=" N   SER B 373 " --> pdb=" O   SER B 369 " (cutoff:3.500A)
      removed outlier: 3.661A  pdb=" N   ILE B 375 " --> pdb=" O   ALA B 371 " (cutoff:3.500A)
      removed outlier: 3.813A  pdb=" N   ASP B 376 " --> pdb=" O   GLY B 372 " (cutoff:3.500A)
      removed outlier: 3.792A  pdb=" N   TRP B 380 " --> pdb=" O   ASP B 376 " (cutoff:3.500A)
      removed outlier: 3.818A  pdb=" N   GLY B 383 " --> pdb=" O   ASN B 379 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 399 through 403
    Processing helix  chain 'B' and resid 409 through 414
      removed outlier: 4.042A  pdb=" N   TRP B 413 " --> pdb=" O   ILE B 410 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 423 through 431
    Processing helix  chain 'B' and resid 433 through 439
      removed outlier: 3.882A  pdb=" N   GLY B 437 " --> pdb=" O   ARG B 434 " (cutoff:3.500A)
      removed outlier: 4.212A  pdb=" N   THR B 438 " --> pdb=" O   LYS B 435 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 495 through 499
    Processing sheet with id=AA1, first strand: chain 'A' and resid 118 through 119
    Processing sheet with id=AA2, first strand: chain 'A' and resid 137 through 139
      removed outlier: 3.757A  pdb=" N   ALA A 178 " --> pdb=" O   LYS A 137 " (cutoff:3.500A)
      removed outlier: 6.309A  pdb=" N   VAL A 147 " --> pdb=" O   ILE A 179 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 251 through 252
      removed outlier: 3.717A  pdb=" N   THR A 493 " --> pdb=" O   TRP A 252 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 476 through 478
      removed outlier: 6.384A  pdb=" N   MET A 444 " --> pdb=" O   ILE A 466 " (cutoff:3.500A)
      removed outlier: 4.648A  pdb=" N   SER A 468 " --> pdb=" O   PHE A 442 " (cutoff:3.500A)
      removed outlier: 6.392A  pdb=" N   PHE A 442 " --> pdb=" O   SER A 468 " (cutoff:3.500A)
      removed outlier: 3.941A  pdb=" N   ALA A 330 " --> pdb=" O   LYS A 447 " (cutoff:3.500A)
      removed outlier: 6.395A  pdb=" N   LEU A 310 " --> pdb=" O   PHE A 331 " (cutoff:3.500A)
      removed outlier: 7.462A  pdb=" N   LEU A 333 " --> pdb=" O   LEU A 310 " (cutoff:3.500A)
      removed outlier: 7.030A  pdb=" N   SER A 312 " --> pdb=" O   LEU A 333 " (cutoff:3.500A)
      removed outlier: 8.667A  pdb=" N   GLU A 335 " --> pdb=" O   SER A 312 " (cutoff:3.500A)
      removed outlier: 6.857A  pdb=" N   ASN A 291 " --> pdb=" O   THR A 309 " (cutoff:3.500A)
      removed outlier: 8.308A  pdb=" N   PHE A 311 " --> pdb=" O   ASN A 291 " (cutoff:3.500A)
      removed outlier: 6.822A  pdb=" N   TYR A 293 " --> pdb=" O   PHE A 311 " (cutoff:3.500A)
      removed outlier: 7.153A  pdb=" N   VAL A 313 " --> pdb=" O   TYR A 293 " (cutoff:3.500A)
      removed outlier: 6.525A  pdb=" N   MET A 295 " --> pdb=" O   VAL A 313 " (cutoff:3.500A)
      removed outlier: 6.055A  pdb=" N   SER A 258 " --> pdb=" O   VAL A 292 " (cutoff:3.500A)
      removed outlier: 7.271A  pdb=" N   ILE A 294 " --> pdb=" O   SER A 258 " (cutoff:3.500A)
      removed outlier: 6.698A  pdb=" N   GLU A 260 " --> pdb=" O   ILE A 294 " (cutoff:3.500A)
      removed outlier: 7.968A  pdb=" N   PHE A 296 " --> pdb=" O   GLU A 260 " (cutoff:3.500A)
      removed outlier: 6.899A  pdb=" N   ALA A 262 " --> pdb=" O   PHE A 296 " (cutoff:3.500A)
      removed outlier: 6.710A  pdb=" N   VAL A 259 " --> pdb=" O   MET B 527 " (cutoff:3.500A)
      removed outlier: 4.872A  pdb=" N   MET B 527 " --> pdb=" O   VAL A 259 " (cutoff:3.500A)
      removed outlier: 4.865A  pdb=" N   MET A 527 " --> pdb=" O   VAL B 259 " (cutoff:3.500A)
      removed outlier: 6.711A  pdb=" N   VAL B 259 " --> pdb=" O   MET A 527 " (cutoff:3.500A)
      removed outlier: 6.057A  pdb=" N   SER B 258 " --> pdb=" O   VAL B 292 " (cutoff:3.500A)
      removed outlier: 7.263A  pdb=" N   ILE B 294 " --> pdb=" O   SER B 258 " (cutoff:3.500A)
      removed outlier: 6.689A  pdb=" N   GLU B 260 " --> pdb=" O   ILE B 294 " (cutoff:3.500A)
      removed outlier: 7.955A  pdb=" N   PHE B 296 " --> pdb=" O   GLU B 260 " (cutoff:3.500A)
      removed outlier: 6.877A  pdb=" N   ALA B 262 " --> pdb=" O   PHE B 296 " (cutoff:3.500A)
      removed outlier: 6.861A  pdb=" N   ASN B 291 " --> pdb=" O   THR B 309 " (cutoff:3.500A)
      removed outlier: 8.348A  pdb=" N   PHE B 311 " --> pdb=" O   ASN B 291 " (cutoff:3.500A)
      removed outlier: 6.873A  pdb=" N   TYR B 293 " --> pdb=" O   PHE B 311 " (cutoff:3.500A)
      removed outlier: 7.176A  pdb=" N   VAL B 313 " --> pdb=" O   TYR B 293 " (cutoff:3.500A)
      removed outlier: 6.550A  pdb=" N   MET B 295 " --> pdb=" O   VAL B 313 " (cutoff:3.500A)
      removed outlier: 6.397A  pdb=" N   LEU B 310 " --> pdb=" O   PHE B 331 " (cutoff:3.500A)
      removed outlier: 7.459A  pdb=" N   LEU B 333 " --> pdb=" O   LEU B 310 " (cutoff:3.500A)
      removed outlier: 7.009A  pdb=" N   SER B 312 " --> pdb=" O   LEU B 333 " (cutoff:3.500A)
      removed outlier: 8.647A  pdb=" N   GLU B 335 " --> pdb=" O   SER B 312 " (cutoff:3.500A)
      removed outlier: 3.948A  pdb=" N   ALA B 330 " --> pdb=" O   LYS B 447 " (cutoff:3.500A)
      removed outlier: 6.359A  pdb=" N   PHE B 442 " --> pdb=" O   SER B 468 " (cutoff:3.500A)
      removed outlier: 4.624A  pdb=" N   SER B 468 " --> pdb=" O   PHE B 442 " (cutoff:3.500A)
      removed outlier: 6.373A  pdb=" N   MET B 444 " --> pdb=" O   ILE B 466 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 338 through 339
    Processing sheet with id=AA6, first strand: chain 'B' and resid 118 through 119
    Processing sheet with id=AA7, first strand: chain 'B' and resid 136 through 139
      removed outlier: 3.732A  pdb=" N   ALA B 178 " --> pdb=" O   LYS B 137 " (cutoff:3.500A)
      removed outlier: 6.290A  pdb=" N   VAL B 147 " --> pdb=" O   ILE B 179 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 251 through 252
      removed outlier: 3.725A  pdb=" N   THR B 493 " --> pdb=" O   TRP B 252 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'B' and resid 338 through 339

    182 hydrogen bonds defined for protein.
    477 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 1.98

  Time building geometry restraints manager: 1.61 seconds

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.

  Histogram of bond lengths:
        1.22 -     1.34: 1970
        1.34 -     1.46: 1328
        1.46 -     1.58: 3012
        1.58 -     1.70: 0
        1.70 -     1.82: 72
  Bond restraints: 6382
  Sorted by residual:
  bond pdb=" C5  NAG B 603 "
       pdb=" O5  NAG B 603 "
    ideal  model  delta    sigma   weight residual
    1.413  1.450 -0.037 2.00e-02 2.50e+03 3.41e+00
  bond pdb=" C5  NAG A 603 "
       pdb=" O5  NAG A 603 "
    ideal  model  delta    sigma   weight residual
    1.413  1.449 -0.036 2.00e-02 2.50e+03 3.27e+00
  bond pdb=" N   MET A 169 "
       pdb=" CA  MET A 169 "
    ideal  model  delta    sigma   weight residual
    1.460  1.486 -0.027 1.54e-02 4.22e+03 3.01e+00
  bond pdb=" CB  LYS B 131 "
       pdb=" CG  LYS B 131 "
    ideal  model  delta    sigma   weight residual
    1.520  1.570 -0.050 3.00e-02 1.11e+03 2.83e+00
  bond pdb=" N   MET B 169 "
       pdb=" CA  MET B 169 "
    ideal  model  delta    sigma   weight residual
    1.460  1.485 -0.026 1.54e-02 4.22e+03 2.75e+00
  ... (remaining 6377 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.93: 8061
        1.93 -     3.85: 462
        3.85 -     5.78: 70
        5.78 -     7.71: 30
        7.71 -     9.63: 13
  Bond angle restraints: 8636
  Sorted by residual:
  angle pdb=" C   ILE B 168 "
        pdb=" N   MET B 169 "
        pdb=" CA  MET B 169 "
      ideal   model   delta    sigma   weight residual
     122.46  130.62   -8.16 1.41e+00 5.03e-01 3.35e+01
  angle pdb=" C   ILE A 168 "
        pdb=" N   MET A 169 "
        pdb=" CA  MET A 169 "
      ideal   model   delta    sigma   weight residual
     122.46  130.40   -7.94 1.41e+00 5.03e-01 3.17e+01
  angle pdb=" N   ILE B 232 "
        pdb=" CA  ILE B 232 "
        pdb=" C   ILE B 232 "
      ideal   model   delta    sigma   weight residual
     109.02  103.98    5.04 9.30e-01 1.16e+00 2.94e+01
  angle pdb=" N   ILE A 232 "
        pdb=" CA  ILE A 232 "
        pdb=" C   ILE A 232 "
      ideal   model   delta    sigma   weight residual
     109.02  104.10    4.92 9.30e-01 1.16e+00 2.80e+01
  angle pdb=" C   GLU A 279 "
        pdb=" N   HIS A 280 "
        pdb=" CA  HIS A 280 "
      ideal   model   delta    sigma   weight residual
     122.19  129.62   -7.43 1.41e+00 5.03e-01 2.78e+01
  ... (remaining 8631 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.50: 3558
       17.50 -    35.01: 315
       35.01 -    52.51: 47
       52.51 -    70.01: 8
       70.01 -    87.51: 4
  Dihedral angle restraints: 3932
    sinusoidal: 1674
      harmonic: 2258
  Sorted by residual:
  dihedral pdb=" CB  CYS B 282 "
           pdb=" SG  CYS B 282 "
           pdb=" SG  CYS B 501 "
           pdb=" CB  CYS B 501 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00 -173.51   87.51     1      1.00e+01 1.00e-02 9.18e+01
  dihedral pdb=" CB  CYS A 282 "
           pdb=" SG  CYS A 282 "
           pdb=" SG  CYS A 501 "
           pdb=" CB  CYS A 501 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00 -172.66   86.66     1      1.00e+01 1.00e-02 9.04e+01
  dihedral pdb=" CA  PHE A 240 "
           pdb=" C   PHE A 240 "
           pdb=" N   PRO A 241 "
           pdb=" CA  PRO A 241 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  158.07   21.93     0      5.00e+00 4.00e-02 1.92e+01
  ... (remaining 3929 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.056: 732
       0.056 -    0.111: 211
       0.111 -    0.167: 48
       0.167 -    0.223: 15
       0.223 -    0.279: 6
  Chirality restraints: 1012
  Sorted by residual:
  chirality pdb=" CB  VAL A 136 "
            pdb=" CA  VAL A 136 "
            pdb=" CG1 VAL A 136 "
            pdb=" CG2 VAL A 136 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.35   -0.28 2.00e-01 2.50e+01 1.94e+00
  chirality pdb=" CB  ILE A 176 "
            pdb=" CA  ILE A 176 "
            pdb=" CG1 ILE A 176 "
            pdb=" CG2 ILE A 176 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.39    0.25 2.00e-01 2.50e+01 1.58e+00
  chirality pdb=" CB  ILE B 176 "
            pdb=" CA  ILE B 176 "
            pdb=" CG1 ILE B 176 "
            pdb=" CG2 ILE B 176 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.40    0.25 2.00e-01 2.50e+01 1.56e+00
  ... (remaining 1009 not shown)

  Planarity restraints: 1092
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  ASN B 485 "    0.031 2.00e-02 2.50e+03   2.83e-02 9.98e+00
        pdb=" CG  ASN B 485 "   -0.030 2.00e-02 2.50e+03
        pdb=" OD1 ASN B 485 "    0.001 2.00e-02 2.50e+03
        pdb=" ND2 ASN B 485 "   -0.033 2.00e-02 2.50e+03
        pdb=" C1  NAG B 603 "    0.032 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  ASN A 485 "   -0.030 2.00e-02 2.50e+03   2.79e-02 9.70e+00
        pdb=" CG  ASN A 485 "    0.030 2.00e-02 2.50e+03
        pdb=" OD1 ASN A 485 "   -0.001 2.00e-02 2.50e+03
        pdb=" ND2 ASN A 485 "    0.033 2.00e-02 2.50e+03
        pdb=" C1  NAG A 603 "   -0.032 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PHE B 240 "   -0.050 5.00e-02 4.00e+02   7.41e-02 8.78e+00
        pdb=" N   PRO B 241 "    0.128 5.00e-02 4.00e+02
        pdb=" CA  PRO B 241 "   -0.036 5.00e-02 4.00e+02
        pdb=" CD  PRO B 241 "   -0.042 5.00e-02 4.00e+02
  ... (remaining 1089 not shown)

  Histogram of nonbonded interaction distances:
        2.44 -     2.93: 2423
        2.93 -     3.42: 5270
        3.42 -     3.92: 9889
        3.92 -     4.41: 11138
        4.41 -     4.90: 19454
  Nonbonded interactions: 48174
  Sorted by model distance:
  nonbonded pdb=" OE2 GLU B 335 "
            pdb=" OG  SER B 365 "
     model   vdw
     2.440 3.040
  nonbonded pdb=" OE2 GLU A 335 "
            pdb=" OG  SER A 365 "
     model   vdw
     2.440 3.040
  nonbonded pdb=" ND2 ASN B 482 "
            pdb=" O   HIS B 486 "
     model   vdw
     2.472 3.120
  nonbonded pdb=" ND2 ASN A 482 "
            pdb=" O   HIS A 486 "
     model   vdw
     2.474 3.120
  nonbonded pdb=" O   VAL B 120 "
            pdb=" N   THR B 127 "
     model   vdw
     2.481 3.120
  ... (remaining 48169 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.03
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'B'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.300
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.270
  Check model and map are aligned:         0.040
  Set scattering table:                    0.080
  Process input model:                     18.650
  Find NCS groups from input model:        0.220
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.650
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   23.250
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7311
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.062   6382  Z= 0.410
  Angle     :  1.111   9.633   8636  Z= 0.606
  Chirality :  0.060   0.279   1012
  Planarity :  0.008   0.074   1086
  Dihedral  : 13.105  83.190   2434
  Min Nonbonded Distance : 2.440

Molprobity Statistics.
  All-atom Clashscore : 1.77
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.95 %
    Favored  : 97.05 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.16 %
    Favored  : 98.84 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -4.21 (0.24), residues: 746
  helix: -4.99 (0.10), residues: 228
  sheet: -1.35 (0.42), residues: 126
  loop : -1.80 (0.25), residues: 392

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.003   TRP A 523 
 HIS   0.007   0.001   HIS A 285 
 PHE   0.047   0.004   PHE B 495 
 TYR   0.011   0.002   TYR A 445 
 ARG   0.006   0.001   ARG B 382 

*********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  1492 Ramachandran restraints generated.
    746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1492 Ramachandran restraints generated.
    746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  65 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 65
  time to evaluate  : 0.603 
Fit side-chains
REVERT: A  361 SER cc_start: 0.8541 (p) cc_final: 0.8336 (p)
REVERT: A  378 MET cc_start: 0.7483 (mmt) cc_final: 0.7216 (mmm)
REVERT: A  411 GLU cc_start: 0.7400 (mm-30) cc_final: 0.7061 (mt-10)
REVERT: B  169 MET cc_start: 0.7198 (ptm) cc_final: 0.6943 (ptp)
REVERT: B  284 MET cc_start: 0.8038 (mmm) cc_final: 0.7797 (mmm)
REVERT: B  361 SER cc_start: 0.8636 (p) cc_final: 0.8410 (p)
REVERT: B  378 MET cc_start: 0.7503 (mmt) cc_final: 0.7241 (mmm)
REVERT: B  411 GLU cc_start: 0.7417 (mm-30) cc_final: 0.7082 (mt-10)
  outliers start: 0
  outliers final: 0
  residues processed: 65
  average time/residue: 0.1926
  time to fit residues: 16.9846
Evaluate side-chains
  58 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 58
  time to evaluate  : 0.672 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 76
   random chunks:
   chunk 64 optimal weight:    2.9990
   chunk 57 optimal weight:    0.9980
   chunk 31 optimal weight:    0.6980
   chunk 19 optimal weight:    1.9990
   chunk 38 optimal weight:    3.9990
   chunk 30 optimal weight:    1.9990
   chunk 59 optimal weight:    1.9990
   chunk 23 optimal weight:    4.9990
   chunk 36 optimal weight:    2.9990
   chunk 44 optimal weight:    0.8980
   chunk 69 optimal weight:    0.0870
   overall best weight:    0.9360

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
A 193 GLN
A 199 GLN
A 248 HIS
A 336 ASN
** B 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 193 GLN
B 199 GLN
B 248 HIS
B 336 ASN

Total number of N/Q/H flips: 8

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4063 r_free = 0.4063 target = 0.193500 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.3850 r_free = 0.3850 target = 0.172148 restraints weight = 6558.557|
|-----------------------------------------------------------------------------|
r_work (start): 0.4006 rms_B_bonded: 1.63
r_work: 0.3900 rms_B_bonded: 2.28 restraints_weight: 0.5000
r_work: 0.3761 rms_B_bonded: 3.94 restraints_weight: 0.2500
r_work (final): 0.3761
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7432
moved from start:          0.1796

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.031   6382  Z= 0.230
  Angle     :  0.535   5.904   8636  Z= 0.285
  Chirality :  0.043   0.145   1012
  Planarity :  0.005   0.062   1086
  Dihedral  :  6.173  51.346    936
  Min Nonbonded Distance : 2.610

Molprobity Statistics.
  All-atom Clashscore : 4.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.88 %
    Favored  : 98.12 %
  Rotamer:
    Outliers :  0.87 %
    Allowed  :  6.40 %
    Favored  : 92.73 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.48 (0.26), residues: 746
  helix: -3.85 (0.18), residues: 246
  sheet: -1.64 (0.42), residues: 142
  loop : -1.23 (0.29), residues: 358

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP B 252 
 HIS   0.002   0.001   HIS B 285 
 PHE   0.018   0.002   PHE A 495 
 TYR   0.014   0.002   TYR A 269 
 ARG   0.002   0.000   ARG B 382 

*********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  1492 Ramachandran restraints generated.
    746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1492 Ramachandran restraints generated.
    746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  78 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 72
  time to evaluate  : 0.705 
Fit side-chains
REVERT: A  361 SER cc_start: 0.8732 (p) cc_final: 0.8501 (p)
REVERT: A  378 MET cc_start: 0.7300 (mmt) cc_final: 0.6975 (mmm)
REVERT: A  411 GLU cc_start: 0.7201 (mm-30) cc_final: 0.6856 (mt-10)
REVERT: B  169 MET cc_start: 0.7463 (ptm) cc_final: 0.7245 (ptm)
REVERT: B  250 MET cc_start: 0.8116 (ttt) cc_final: 0.7802 (ttm)
REVERT: B  361 SER cc_start: 0.8705 (p) cc_final: 0.8474 (p)
REVERT: B  378 MET cc_start: 0.7360 (mmt) cc_final: 0.7027 (mmm)
REVERT: B  411 GLU cc_start: 0.7180 (mm-30) cc_final: 0.6856 (mt-10)
REVERT: B  494 LYS cc_start: 0.8598 (mttt) cc_final: 0.8294 (mmtm)
  outliers start: 6
  outliers final: 4
  residues processed: 74
  average time/residue: 0.1703
  time to fit residues: 17.5767
Evaluate side-chains
  74 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 70
  time to evaluate  : 0.685 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  342 THR
Chi-restraints excluded: chain A residue  464 ARG
Chi-restraints excluded: chain B residue  342 THR
Chi-restraints excluded: chain B residue  464 ARG
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 76
   random chunks:
   chunk 32 optimal weight:    2.9990
   chunk 40 optimal weight:    0.3980
   chunk 58 optimal weight:    2.9990
   chunk 62 optimal weight:    0.9980
   chunk 36 optimal weight:    0.8980
   chunk 46 optimal weight:    0.9990
   chunk 61 optimal weight:    0.6980
   chunk 54 optimal weight:    0.6980
   chunk 45 optimal weight:    0.7980
   chunk 30 optimal weight:    2.9990
   chunk 4 optimal weight:    1.9990
   overall best weight:    0.6980

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
A 193 GLN
A 270 ASN
** B 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 193 GLN
B 270 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4094 r_free = 0.4094 target = 0.195089 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3861 r_free = 0.3861 target = 0.171128 restraints weight = 6572.804|
|-----------------------------------------------------------------------------|
r_work (start): 0.3969 rms_B_bonded: 1.93
r_work: 0.3846 rms_B_bonded: 2.78 restraints_weight: 0.5000
r_work: 0.3697 rms_B_bonded: 4.80 restraints_weight: 0.2500
r_work (final): 0.3697
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7571
moved from start:          0.2230

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.025   6382  Z= 0.174
  Angle     :  0.458   4.510   8636  Z= 0.243
  Chirality :  0.042   0.141   1012
  Planarity :  0.004   0.044   1086
  Dihedral  :  5.683  52.043    936
  Min Nonbonded Distance : 2.602

Molprobity Statistics.
  All-atom Clashscore : 4.10
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.82 %
    Favored  : 97.18 %
  Rotamer:
    Outliers :  0.44 %
    Allowed  :  9.01 %
    Favored  : 90.55 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.45 (0.28), residues: 746
  helix: -2.30 (0.27), residues: 248
  sheet: -1.76 (0.41), residues: 144
  loop : -0.82 (0.32), residues: 354

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP B 252 
 HIS   0.002   0.001   HIS A 285 
 PHE   0.019   0.001   PHE B 495 
 TYR   0.009   0.001   TYR B 269 
 ARG   0.001   0.000   ARG B 317 

*********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  1492 Ramachandran restraints generated.
    746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1492 Ramachandran restraints generated.
    746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  81 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 78
  time to evaluate  : 0.762 
Fit side-chains
REVERT: A  250 MET cc_start: 0.8250 (ttt) cc_final: 0.7986 (ttp)
REVERT: A  267 GLU cc_start: 0.8327 (mt-10) cc_final: 0.8101 (mt-10)
REVERT: A  411 GLU cc_start: 0.7295 (mm-30) cc_final: 0.6902 (mt-10)
REVERT: A  435 LYS cc_start: 0.7763 (mttt) cc_final: 0.7549 (mttp)
REVERT: B  164 GLN cc_start: 0.7877 (mm-40) cc_final: 0.7674 (mm-40)
REVERT: B  250 MET cc_start: 0.8231 (ttt) cc_final: 0.7991 (ttm)
REVERT: B  267 GLU cc_start: 0.8381 (mt-10) cc_final: 0.8162 (mt-10)
REVERT: B  284 MET cc_start: 0.8285 (mmm) cc_final: 0.8075 (mmm)
REVERT: B  411 GLU cc_start: 0.7287 (mm-30) cc_final: 0.6903 (mt-10)
REVERT: B  494 LYS cc_start: 0.8714 (mttt) cc_final: 0.8489 (mmtm)
  outliers start: 3
  outliers final: 3
  residues processed: 78
  average time/residue: 0.1876
  time to fit residues: 19.9390
Evaluate side-chains
  74 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 71
  time to evaluate  : 0.707 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  464 ARG
Chi-restraints excluded: chain B residue  136 VAL
Chi-restraints excluded: chain B residue  464 ARG
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 76
   random chunks:
   chunk 74 optimal weight:    0.0370
   chunk 11 optimal weight:    0.6980
   chunk 73 optimal weight:    1.9990
   chunk 42 optimal weight:    2.9990
   chunk 32 optimal weight:    1.9990
   chunk 5 optimal weight:    2.9990
   chunk 14 optimal weight:    0.9990
   chunk 33 optimal weight:    0.6980
   chunk 54 optimal weight:    4.9990
   chunk 2 optimal weight:    1.9990
   chunk 0 optimal weight:    3.9990
   overall best weight:    0.8862

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
A 270 ASN
A 298 ASN
** B 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 270 ASN
B 298 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4149 r_free = 0.4149 target = 0.199137 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3913 r_free = 0.3913 target = 0.174526 restraints weight = 6539.784|
|-----------------------------------------------------------------------------|
r_work (start): 0.3832 rms_B_bonded: 2.00
r_work: 0.3710 rms_B_bonded: 2.81 restraints_weight: 0.5000
r_work: 0.3560 rms_B_bonded: 4.84 restraints_weight: 0.2500
r_work (final): 0.3560
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7597
moved from start:          0.2610

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   6382  Z= 0.211
  Angle     :  0.480   5.079   8636  Z= 0.252
  Chirality :  0.042   0.140   1012
  Planarity :  0.003   0.036   1086
  Dihedral  :  5.674  51.402    936
  Min Nonbonded Distance : 2.613

Molprobity Statistics.
  All-atom Clashscore : 4.34
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.82 %
    Favored  : 97.18 %
  Rotamer:
    Outliers :  0.58 %
    Allowed  : 10.47 %
    Favored  : 88.95 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.83 (0.30), residues: 746
  helix: -1.56 (0.31), residues: 248
  sheet: -1.80 (0.43), residues: 126
  loop : -0.56 (0.33), residues: 372

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 252 
 HIS   0.002   0.001   HIS B 285 
 PHE   0.020   0.001   PHE B 495 
 TYR   0.010   0.001   TYR A 398 
 ARG   0.001   0.000   ARG A 317 

*********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  1492 Ramachandran restraints generated.
    746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1492 Ramachandran restraints generated.
    746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  74 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 70
  time to evaluate  : 0.817 
Fit side-chains
REVERT: A  250 MET cc_start: 0.8260 (ttt) cc_final: 0.7977 (ttp)
REVERT: A  435 LYS cc_start: 0.7914 (mttt) cc_final: 0.7646 (mttp)
  outliers start: 4
  outliers final: 2
  residues processed: 72
  average time/residue: 0.1851
  time to fit residues: 18.2676
Evaluate side-chains
  68 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 66
  time to evaluate  : 0.697 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  342 THR
Chi-restraints excluded: chain B residue  342 THR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 76
   random chunks:
   chunk 68 optimal weight:    7.9990
   chunk 40 optimal weight:    2.9990
   chunk 5 optimal weight:    1.9990
   chunk 19 optimal weight:    2.9990
   chunk 28 optimal weight:    2.9990
   chunk 54 optimal weight:    0.7980
   chunk 11 optimal weight:    2.9990
   chunk 14 optimal weight:    4.9990
   chunk 43 optimal weight:    2.9990
   chunk 61 optimal weight:    3.9990
   chunk 13 optimal weight:    1.9990
   overall best weight:    2.1588

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4127 r_free = 0.4127 target = 0.196531 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3877 r_free = 0.3877 target = 0.170893 restraints weight = 6560.067|
|-----------------------------------------------------------------------------|
r_work (start): 0.3765 rms_B_bonded: 2.03
r_work: 0.3642 rms_B_bonded: 2.80 restraints_weight: 0.5000
r_work: 0.3490 rms_B_bonded: 4.79 restraints_weight: 0.2500
r_work (final): 0.3490
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7720
moved from start:          0.3214

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.061   6382  Z= 0.461
  Angle     :  0.677   6.937   8636  Z= 0.352
  Chirality :  0.048   0.143   1012
  Planarity :  0.004   0.039   1086
  Dihedral  :  6.374  49.712    936
  Min Nonbonded Distance : 2.544

Molprobity Statistics.
  All-atom Clashscore : 6.11
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.29 %
    Favored  : 95.71 %
  Rotamer:
    Outliers :  2.18 %
    Allowed  : 12.06 %
    Favored  : 85.76 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.19 (0.30), residues: 746
  helix: -1.72 (0.30), residues: 248
  sheet: -2.16 (0.42), residues: 128
  loop : -0.81 (0.33), residues: 370

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.002   TRP B 252 
 HIS   0.003   0.001   HIS B 280 
 PHE   0.025   0.003   PHE A 495 
 TYR   0.021   0.003   TYR A 398 
 ARG   0.003   0.000   ARG A 434 

*********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  1492 Ramachandran restraints generated.
    746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1492 Ramachandran restraints generated.
    746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  99 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 84
  time to evaluate  : 0.677 
Fit side-chains
REVERT: A  250 MET cc_start: 0.8336 (OUTLIER) cc_final: 0.8008 (ttp)
REVERT: A  274 GLU cc_start: 0.7172 (tt0) cc_final: 0.6911 (pt0)
REVERT: A  355 GLU cc_start: 0.8096 (tm-30) cc_final: 0.7769 (mm-30)
REVERT: B  171 ASP cc_start: 0.6921 (p0) cc_final: 0.6536 (t0)
  outliers start: 15
  outliers final: 6
  residues processed: 92
  average time/residue: 0.1800
  time to fit residues: 22.6440
Evaluate side-chains
  87 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 80
  time to evaluate  : 0.704 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  144 VAL
Chi-restraints excluded: chain A residue  250 MET
Chi-restraints excluded: chain A residue  342 THR
Chi-restraints excluded: chain A residue  527 MET
Chi-restraints excluded: chain B residue  144 VAL
Chi-restraints excluded: chain B residue  342 THR
Chi-restraints excluded: chain B residue  527 MET
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 76
   random chunks:
   chunk 46 optimal weight:    1.9990
   chunk 43 optimal weight:    0.7980
   chunk 37 optimal weight:    0.9990
   chunk 58 optimal weight:    0.3980
   chunk 12 optimal weight:    0.6980
   chunk 41 optimal weight:    0.9980
   chunk 65 optimal weight:    0.9990
   chunk 28 optimal weight:    1.9990
   chunk 26 optimal weight:    1.9990
   chunk 45 optimal weight:    0.7980
   chunk 40 optimal weight:    3.9990
   overall best weight:    0.7380

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
A 270 ASN
B 270 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4038 r_free = 0.4038 target = 0.190861 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3788 r_free = 0.3788 target = 0.164998 restraints weight = 6652.756|
|-----------------------------------------------------------------------------|
r_work (start): 0.3828 rms_B_bonded: 2.11
r_work: 0.3708 rms_B_bonded: 2.87 restraints_weight: 0.5000
r_work: 0.3550 rms_B_bonded: 4.98 restraints_weight: 0.2500
r_work (final): 0.3550
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7641
moved from start:          0.3212

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   6382  Z= 0.187
  Angle     :  0.488   6.874   8636  Z= 0.253
  Chirality :  0.042   0.139   1012
  Planarity :  0.003   0.032   1086
  Dihedral  :  5.761  52.156    936
  Min Nonbonded Distance : 2.588

Molprobity Statistics.
  All-atom Clashscore : 5.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.55 %
    Favored  : 97.45 %
  Rotamer:
    Outliers :  1.89 %
    Allowed  : 13.81 %
    Favored  : 84.30 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.65 (0.31), residues: 746
  helix: -1.02 (0.33), residues: 248
  sheet: -1.94 (0.41), residues: 148
  loop : -0.54 (0.35), residues: 350

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP B 252 
 HIS   0.002   0.001   HIS B 285 
 PHE   0.023   0.001   PHE A 495 
 TYR   0.009   0.001   TYR B 204 
 ARG   0.002   0.000   ARG B 277 

*********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  1492 Ramachandran restraints generated.
    746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1492 Ramachandran restraints generated.
    746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  89 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 76
  time to evaluate  : 0.712 
Fit side-chains
REVERT: A  250 MET cc_start: 0.8317 (ttt) cc_final: 0.8052 (ttp)
REVERT: A  278 GLN cc_start: 0.7119 (OUTLIER) cc_final: 0.6755 (mp10)
REVERT: B  171 ASP cc_start: 0.6813 (p0) cc_final: 0.6421 (t0)
REVERT: B  250 MET cc_start: 0.8304 (ttt) cc_final: 0.8069 (ttp)
REVERT: B  278 GLN cc_start: 0.7053 (OUTLIER) cc_final: 0.6687 (mp10)
  outliers start: 13
  outliers final: 5
  residues processed: 85
  average time/residue: 0.1652
  time to fit residues: 19.8203
Evaluate side-chains
  80 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 73
  time to evaluate  : 0.903 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  278 GLN
Chi-restraints excluded: chain A residue  332 VAL
Chi-restraints excluded: chain A residue  342 THR
Chi-restraints excluded: chain B residue  278 GLN
Chi-restraints excluded: chain B residue  286 PHE
Chi-restraints excluded: chain B residue  332 VAL
Chi-restraints excluded: chain B residue  342 THR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 76
   random chunks:
   chunk 57 optimal weight:    3.9990
   chunk 62 optimal weight:    0.4980
   chunk 38 optimal weight:    4.9990
   chunk 39 optimal weight:    0.9990
   chunk 10 optimal weight:    6.9990
   chunk 71 optimal weight:    3.9990
   chunk 52 optimal weight:    5.9990
   chunk 65 optimal weight:    0.8980
   chunk 45 optimal weight:    5.9990
   chunk 44 optimal weight:    2.9990
   chunk 29 optimal weight:    5.9990
   overall best weight:    1.8786

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3961 r_free = 0.3961 target = 0.183205 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3719 r_free = 0.3719 target = 0.159408 restraints weight = 6606.389|
|-----------------------------------------------------------------------------|
r_work (start): 0.3726 rms_B_bonded: 1.92
r_work: 0.3615 rms_B_bonded: 2.60 restraints_weight: 0.5000
r_work: 0.3466 rms_B_bonded: 4.44 restraints_weight: 0.2500
r_work (final): 0.3466
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7649
moved from start:          0.3517

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.054   6382  Z= 0.399
  Angle     :  0.618   6.002   8636  Z= 0.324
  Chirality :  0.046   0.139   1012
  Planarity :  0.004   0.034   1086
  Dihedral  :  6.231  50.243    936
  Min Nonbonded Distance : 2.574

Molprobity Statistics.
  All-atom Clashscore : 6.03
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.42 %
    Favored  : 95.58 %
  Rotamer:
    Outliers :  3.05 %
    Allowed  : 13.23 %
    Favored  : 83.72 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.91 (0.31), residues: 746
  helix: -1.23 (0.32), residues: 248
  sheet: -2.17 (0.41), residues: 144
  loop : -0.67 (0.34), residues: 354

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.002   TRP B 252 
 HIS   0.003   0.001   HIS A 388 
 PHE   0.024   0.002   PHE A 495 
 TYR   0.018   0.002   TYR A 398 
 ARG   0.002   0.000   ARG A 177 

*********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  1492 Ramachandran restraints generated.
    746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1492 Ramachandran restraints generated.
    746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  102 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 81
  time to evaluate  : 0.642 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  250 MET cc_start: 0.8306 (OUTLIER) cc_final: 0.7969 (ttp)
REVERT: A  426 GLU cc_start: 0.6706 (tt0) cc_final: 0.6480 (tp30)
REVERT: B  171 ASP cc_start: 0.6934 (p0) cc_final: 0.6490 (t0)
  outliers start: 21
  outliers final: 13
  residues processed: 98
  average time/residue: 0.1689
  time to fit residues: 22.5060
Evaluate side-chains
  91 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 77
  time to evaluate  : 0.640 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  144 VAL
Chi-restraints excluded: chain A residue  250 MET
Chi-restraints excluded: chain A residue  278 GLN
Chi-restraints excluded: chain A residue  281 MET
Chi-restraints excluded: chain A residue  286 PHE
Chi-restraints excluded: chain A residue  332 VAL
Chi-restraints excluded: chain A residue  342 THR
Chi-restraints excluded: chain A residue  493 THR
Chi-restraints excluded: chain B residue  136 VAL
Chi-restraints excluded: chain B residue  144 VAL
Chi-restraints excluded: chain B residue  278 GLN
Chi-restraints excluded: chain B residue  286 PHE
Chi-restraints excluded: chain B residue  332 VAL
Chi-restraints excluded: chain B residue  342 THR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 76
   random chunks:
   chunk 37 optimal weight:    0.6980
   chunk 66 optimal weight:    2.9990
   chunk 32 optimal weight:    0.9980
   chunk 56 optimal weight:    2.9990
   chunk 36 optimal weight:    2.9990
   chunk 53 optimal weight:    0.9990
   chunk 2 optimal weight:    0.9990
   chunk 58 optimal weight:    0.9990
   chunk 40 optimal weight:    0.3980
   chunk 0 optimal weight:    3.9990
   chunk 30 optimal weight:    5.9990
   overall best weight:    0.8184

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
A 270 ASN
B 270 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4161 r_free = 0.4161 target = 0.200919 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3922 r_free = 0.3922 target = 0.176232 restraints weight = 6402.013|
|-----------------------------------------------------------------------------|
r_work (start): 0.3892 rms_B_bonded: 1.99
r_work: 0.3781 rms_B_bonded: 2.70 restraints_weight: 0.5000
r_work: 0.3630 rms_B_bonded: 4.65 restraints_weight: 0.2500
r_work (final): 0.3630
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7622
moved from start:          0.3475

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   6382  Z= 0.199
  Angle     :  0.484   5.934   8636  Z= 0.255
  Chirality :  0.042   0.139   1012
  Planarity :  0.003   0.033   1086
  Dihedral  :  5.786  52.152    936
  Min Nonbonded Distance : 2.577

Molprobity Statistics.
  All-atom Clashscore : 5.38
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.68 %
    Favored  : 97.32 %
  Rotamer:
    Outliers :  2.03 %
    Allowed  : 15.41 %
    Favored  : 82.56 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.53 (0.32), residues: 746
  helix: -0.82 (0.33), residues: 248
  sheet: -2.16 (0.37), residues: 162
  loop : -0.31 (0.37), residues: 336

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP B 252 
 HIS   0.001   0.001   HIS B 285 
 PHE   0.024   0.001   PHE A 495 
 TYR   0.010   0.001   TYR A 204 
 ARG   0.002   0.000   ARG B 277 

*********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  1492 Ramachandran restraints generated.
    746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1492 Ramachandran restraints generated.
    746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  86 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 72
  time to evaluate  : 0.664 
Fit side-chains
REVERT: A  250 MET cc_start: 0.8294 (ttt) cc_final: 0.8026 (ttp)
REVERT: A  278 GLN cc_start: 0.6990 (OUTLIER) cc_final: 0.6596 (mp10)
REVERT: B  171 ASP cc_start: 0.6888 (p0) cc_final: 0.6420 (t0)
REVERT: B  250 MET cc_start: 0.8278 (ttt) cc_final: 0.8020 (ttp)
REVERT: B  278 GLN cc_start: 0.7001 (OUTLIER) cc_final: 0.6605 (mp10)
  outliers start: 14
  outliers final: 7
  residues processed: 81
  average time/residue: 0.1713
  time to fit residues: 19.3325
Evaluate side-chains
  78 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 69
  time to evaluate  : 0.710 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  278 GLN
Chi-restraints excluded: chain A residue  295 MET
Chi-restraints excluded: chain A residue  332 VAL
Chi-restraints excluded: chain A residue  342 THR
Chi-restraints excluded: chain B residue  278 GLN
Chi-restraints excluded: chain B residue  286 PHE
Chi-restraints excluded: chain B residue  295 MET
Chi-restraints excluded: chain B residue  332 VAL
Chi-restraints excluded: chain B residue  342 THR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 76
   random chunks:
   chunk 69 optimal weight:    0.5980
   chunk 54 optimal weight:    0.9980
   chunk 39 optimal weight:    4.9990
   chunk 2 optimal weight:    0.5980
   chunk 29 optimal weight:    2.9990
   chunk 15 optimal weight:    3.9990
   chunk 31 optimal weight:    0.6980
   chunk 42 optimal weight:    0.7980
   chunk 33 optimal weight:    3.9990
   chunk 48 optimal weight:    5.9990
   chunk 13 optimal weight:    1.9990
   overall best weight:    0.7380

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
A 270 ASN
B 270 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4072 r_free = 0.4072 target = 0.192645 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3844 r_free = 0.3844 target = 0.169233 restraints weight = 6614.735|
|-----------------------------------------------------------------------------|
r_work (start): 0.3934 rms_B_bonded: 1.91
r_work: 0.3817 rms_B_bonded: 2.70 restraints_weight: 0.5000
r_work: 0.3666 rms_B_bonded: 4.65 restraints_weight: 0.2500
r_work (final): 0.3666
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7612
moved from start:          0.3529

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   6382  Z= 0.184
  Angle     :  0.461   4.941   8636  Z= 0.244
  Chirality :  0.042   0.138   1012
  Planarity :  0.003   0.032   1086
  Dihedral  :  5.614  51.660    936
  Min Nonbonded Distance : 2.592

Molprobity Statistics.
  All-atom Clashscore : 4.82
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.95 %
    Favored  : 97.05 %
  Rotamer:
    Outliers :  1.60 %
    Allowed  : 16.13 %
    Favored  : 82.27 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.33 (0.32), residues: 746
  helix: -0.50 (0.34), residues: 248
  sheet: -2.15 (0.37), residues: 162
  loop : -0.26 (0.37), residues: 336

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP B 252 
 HIS   0.002   0.001   HIS B 285 
 PHE   0.023   0.001   PHE B 495 
 TYR   0.009   0.001   TYR A 204 
 ARG   0.002   0.000   ARG B 277 

*********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  1492 Ramachandran restraints generated.
    746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1492 Ramachandran restraints generated.
    746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  84 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 73
  time to evaluate  : 0.652 
Fit side-chains
REVERT: A  250 MET cc_start: 0.8274 (ttt) cc_final: 0.7985 (ttp)
REVERT: A  278 GLN cc_start: 0.7095 (OUTLIER) cc_final: 0.6710 (mp10)
REVERT: B  171 ASP cc_start: 0.6877 (p0) cc_final: 0.6392 (t0)
REVERT: B  250 MET cc_start: 0.8271 (ttt) cc_final: 0.8002 (ttp)
REVERT: B  278 GLN cc_start: 0.7067 (OUTLIER) cc_final: 0.6691 (mp10)
  outliers start: 11
  outliers final: 7
  residues processed: 80
  average time/residue: 0.1635
  time to fit residues: 18.6704
Evaluate side-chains
  80 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 71
  time to evaluate  : 1.002 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  278 GLN
Chi-restraints excluded: chain A residue  295 MET
Chi-restraints excluded: chain A residue  332 VAL
Chi-restraints excluded: chain A residue  342 THR
Chi-restraints excluded: chain B residue  278 GLN
Chi-restraints excluded: chain B residue  286 PHE
Chi-restraints excluded: chain B residue  295 MET
Chi-restraints excluded: chain B residue  332 VAL
Chi-restraints excluded: chain B residue  342 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 76
   random chunks:
   chunk 74 optimal weight:    2.9990
   chunk 40 optimal weight:    2.9990
   chunk 17 optimal weight:    1.9990
   chunk 60 optimal weight:    0.0170
   chunk 68 optimal weight:    4.9990
   chunk 35 optimal weight:    0.4980
   chunk 58 optimal weight:    0.5980
   chunk 14 optimal weight:    4.9990
   chunk 44 optimal weight:    0.9980
   chunk 66 optimal weight:    1.9990
   chunk 65 optimal weight:    0.9980
   overall best weight:    0.6218

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
A 270 ASN
B 270 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4134 r_free = 0.4134 target = 0.198541 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3896 r_free = 0.3896 target = 0.173539 restraints weight = 6526.747|
|-----------------------------------------------------------------------------|
r_work (start): 0.3887 rms_B_bonded: 2.07
r_work: 0.3780 rms_B_bonded: 2.72 restraints_weight: 0.5000
r_work: 0.3629 rms_B_bonded: 4.70 restraints_weight: 0.2500
r_work (final): 0.3629
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7589
moved from start:          0.3561

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.025   6382  Z= 0.163
  Angle     :  0.448   4.902   8636  Z= 0.237
  Chirality :  0.041   0.138   1012
  Planarity :  0.003   0.032   1086
  Dihedral  :  5.518  51.985    936
  Min Nonbonded Distance : 2.594

Molprobity Statistics.
  All-atom Clashscore : 5.14
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.41 %
    Favored  : 97.59 %
  Rotamer:
    Outliers :  1.45 %
    Allowed  : 16.42 %
    Favored  : 82.12 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.17 (0.32), residues: 746
  helix: -0.33 (0.34), residues: 248
  sheet: -2.02 (0.37), residues: 166
  loop : -0.19 (0.38), residues: 332

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A 252 
 HIS   0.002   0.001   HIS B 285 
 PHE   0.022   0.001   PHE A 495 
 TYR   0.011   0.001   TYR B 204 
 ARG   0.002   0.000   ARG A 317 

********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  1492 Ramachandran restraints generated.
    746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1492 Ramachandran restraints generated.
    746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  80 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 70
  time to evaluate  : 0.602 
Fit side-chains
REVERT: A  250 MET cc_start: 0.8280 (ttt) cc_final: 0.7996 (ttp)
REVERT: A  278 GLN cc_start: 0.7056 (OUTLIER) cc_final: 0.6696 (mp10)
REVERT: B  171 ASP cc_start: 0.6886 (p0) cc_final: 0.6380 (t0)
REVERT: B  218 LEU cc_start: 0.8355 (mt) cc_final: 0.8153 (mp)
REVERT: B  250 MET cc_start: 0.8267 (ttt) cc_final: 0.8006 (ttp)
REVERT: B  278 GLN cc_start: 0.7015 (OUTLIER) cc_final: 0.6662 (mp10)
  outliers start: 10
  outliers final: 7
  residues processed: 77
  average time/residue: 0.1603
  time to fit residues: 17.3050
Evaluate side-chains
  77 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 68
  time to evaluate  : 0.742 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  278 GLN
Chi-restraints excluded: chain A residue  295 MET
Chi-restraints excluded: chain A residue  332 VAL
Chi-restraints excluded: chain A residue  342 THR
Chi-restraints excluded: chain B residue  278 GLN
Chi-restraints excluded: chain B residue  295 MET
Chi-restraints excluded: chain B residue  332 VAL
Chi-restraints excluded: chain B residue  342 THR
Chi-restraints excluded: chain B residue  463 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 76
   random chunks:
   chunk 45 optimal weight:    0.9990
   chunk 2 optimal weight:    0.4980
   chunk 56 optimal weight:    3.9990
   chunk 47 optimal weight:    1.9990
   chunk 43 optimal weight:    3.9990
   chunk 7 optimal weight:    0.5980
   chunk 71 optimal weight:    2.9990
   chunk 40 optimal weight:    0.9980
   chunk 3 optimal weight:    0.9980
   chunk 74 optimal weight:    2.9990
   chunk 73 optimal weight:    0.7980
   overall best weight:    0.7780

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
A 270 ASN
B 270 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4126 r_free = 0.4126 target = 0.197673 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3884 r_free = 0.3884 target = 0.172371 restraints weight = 6569.167|
|-----------------------------------------------------------------------------|
r_work (start): 0.3840 rms_B_bonded: 2.11
r_work: 0.3726 rms_B_bonded: 2.83 restraints_weight: 0.5000
r_work: 0.3571 rms_B_bonded: 4.87 restraints_weight: 0.2500
r_work (final): 0.3571
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7609
moved from start:          0.3596

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   6382  Z= 0.192
  Angle     :  0.468   4.859   8636  Z= 0.247
  Chirality :  0.042   0.139   1012
  Planarity :  0.003   0.032   1086
  Dihedral  :  5.593  51.609    936
  Min Nonbonded Distance : 2.591

Molprobity Statistics.
  All-atom Clashscore : 5.06
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.41 %
    Favored  : 97.59 %
  Rotamer:
    Outliers :  1.89 %
    Allowed  : 16.28 %
    Favored  : 81.83 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.13 (0.32), residues: 746
  helix: -0.30 (0.34), residues: 248
  sheet: -2.00 (0.37), residues: 162
  loop : -0.20 (0.37), residues: 336

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 252 
 HIS   0.002   0.001   HIS B 285 
 PHE   0.023   0.001   PHE B 495 
 TYR   0.010   0.001   TYR B 204 
 ARG   0.003   0.000   ARG A 317 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3412.88 seconds
wall clock time: 61 minutes 11.76 seconds (3671.76 seconds total)